Not from an overwatering from drip system.
Overwatering from your drippers would effect the whole plant-roots first then on up...
Spots like that from water is usually from getting water on the pepper and it magnifies the suns heat or whatever causing a burn or in humid conditions causes rotting.
I'd go with sun scald.
If it started elsewhere on the pods and in a shaded area I'd guess a calcium problem,possibly.Calcium problems cause the pods to rot and drop sometimes.
But if you had a good bud set then you probably don't have a calcium problem.

smokemaster, I've seen you comment several times on calcium deficiency in pepper plants, so when I potted up my peppers earlier this spring I included crushed oyster shells in the mostly inorganic bottom layer of the pot. Worked fine, however I should have first asked the question...How does calcium affect pepper plants and is there a need to quantify the addition?

I think C.Chinense use more calcium than other kinds of peppers.
A lack of calcium usually causes wrinkled leaves and blossum drop and or a lack of blossoms.
Magnesium and calcium both are taken up by the same receptors in a plant so too much of either can cause a shortage in the other.
I use Dolomite lime because it is both ca. and mag.

For budding and budset I add some dolomite lime to 5% white Vinegar to make Calcium/Mag. Acetate.
It's what they sell as blossom set in the little spray bottles for way too much $ an oz.
I use it just like you would use the commercial stuff or can use it as aqn addition to your ferts.
I mix 2-3 oz. of it with 1gal. of water for a soil drench or to folier feed.
Watch out that you don't use it too much.It is possible to change the soil in pots PH with large doses but I water my pots until they flood out the bottom so I'm probably flushing out anything that is water soluable every time I water.

From what I've read,in general most people add at least some lime or whatever to their potting mixes but it's debatable if you really have to.
People in some places have well water that has tons of ca. in it.
Plants don't need that much Ca. and in the form of shells or powders it takes at least a slightly acid soil to make these forms of ca. plant usable.
I find that for me using my homemade soil mixes that adding ca. makes a difference.Your milage may vary...
I do think that Calcium Acetate does help out a lot with budingand budset.
To make the Acetate I just put an inch of powdered Dolomite lime in a quart cottage cheese type container and fill it with 5% white vinegar(only use white vinegar).
Don't cap it tightly or the top pops off-it gives off a gas when the vinegar reacts with the ca.
I stir it and add more vinegar as I use the stuff until most of the lime is gone.

Some interesting chemistry there smokemaster...I can appreciate that. It's a bit complicated but I use both top and bottom watering for my potted hot pepper plants depending on location of the plants. Indoors I actually use both methods, preferring to bottom water with a small amount of fertilizer, then once I week I top water to flush any excess fertilizer. I keep 32 potted pepper plants in a 4' x 8' raised bed during the warmer months. This bed is dug down to a depth of four feet to the top of the treated lumber sides of the raised bed and covered at night and cool days with three glass window panes. We can get as much as a 40 degree swing in temperatures during the spring and fall months. I top water these pepper plants while in the raised beds. The bottom of the raised bed is covered in a six inch layer of wood chip fines to assist in drainage of the pots. Once removed indoors for the winter I use a plastic pot to hold the water for bottom watering and after flushing the plants I place them in a similar pot with wood chip fines for a day to assist in drainage. May seem like a pretty complicated process, but it appears to be working. I don't know any other way to grow hot peppers in our cool, short season other than a heated greenhouse which I can't justify for 30 pepper plants.

As a side note smokemaster you brought back an old memory of the time I got suspended from my high school chemistry class for dropping a Zn nugget in the sulfuric acid bottle. Didn't hold me back though...always wanted to be a chemist.